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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Shewanella woodyi (strain ATCC 51908 / MS32)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121SubstrateUniRule annotation
Binding sitei45 – 451SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei162 – 1621SubstrateUniRule annotation
Sitei164 – 1641Important for catalytic activityUniRule annotation
Binding sitei195 – 1951SubstrateUniRule annotation
Sitei213 – 2131Important for catalytic activityUniRule annotation
Active sitei222 – 2221Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciSWOO392500:GI2C-504-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:Swoo_0487
OrganismiShewanella woodyi (strain ATCC 51908 / MS32)
Taxonomic identifieri392500 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000002168 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 279279Diaminopimelate epimerasePRO_1000099267Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 222

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi392500.Swoo_0487.

Structurei

3D structure databases

ProteinModelPortaliB1KQD0.
SMRiB1KQD0. Positions 2-277.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 102Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni213 – 2142Substrate bindingUniRule annotation
Regioni223 – 2242Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B1KQD0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIHFAKMHGL GNDFMVVDGV TQNVFFSPEQ IKRLADRNFG VGFDQLLLVE
60 70 80 90 100
PPYDPDLDFH YRIFNADGGE VEQCGNGARC FARFVRNKGL TNKHKIKVST
110 120 130 140 150
SNGKITLRLE RDGNVTVNMG VPVLDPSKIP FNAKRVEKTY LLQTSSSHAM
160 170 180 190 200
ETFLCGAISM GNPHCVLEVE DIEHAEVERI GALLTQNERF PKGVNVGFMQ
210 220 230 240 250
VIDAGHIKLR VYERGAAETL ACGTGACAAA AVGQLQGKLN KMVRVDLPGG
260 270
TLTINWEGEG NPLWMTGPAE HVYDGQIPQ
Length:279
Mass (Da):30,626
Last modified:April 28, 2008 - v1
Checksum:i2D865DEF34E6E969
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000961 Genomic DNA. Translation: ACA84785.1.
RefSeqiYP_001758880.1. NC_010506.1.

Genome annotation databases

EnsemblBacteriaiACA84785; ACA84785; Swoo_0487.
KEGGiswd:Swoo_0487.
PATRICi23603223. VBISheWoo126588_0508.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000961 Genomic DNA. Translation: ACA84785.1.
RefSeqiYP_001758880.1. NC_010506.1.

3D structure databases

ProteinModelPortaliB1KQD0.
SMRiB1KQD0. Positions 2-277.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi392500.Swoo_0487.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA84785; ACA84785; Swoo_0487.
KEGGiswd:Swoo_0487.
PATRICi23603223. VBISheWoo126588_0508.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciSWOO392500:GI2C-504-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51908 / MS32.

Entry informationi

Entry nameiDAPF_SHEWM
AccessioniPrimary (citable) accession number: B1KQD0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 23, 2009
Last sequence update: April 28, 2008
Last modified: March 31, 2015
This is version 54 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.